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\name{nearest-methods}
\alias{nearest-methods}
\alias{precede}
\alias{precede,RangedSummarizedExperiment,ANY-method}
\alias{precede,ANY,RangedSummarizedExperiment-method}
\alias{precede,RangedSummarizedExperiment,RangedSummarizedExperiment-method}
\alias{follow}
\alias{follow,RangedSummarizedExperiment,ANY-method}
\alias{follow,ANY,RangedSummarizedExperiment-method}
\alias{follow,RangedSummarizedExperiment,RangedSummarizedExperiment-method}
\alias{nearest}
\alias{nearest,RangedSummarizedExperiment,ANY-method}
\alias{nearest,ANY,RangedSummarizedExperiment-method}
\alias{nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method}
\alias{distance}
\alias{distance,RangedSummarizedExperiment,ANY-method}
\alias{distance,ANY,RangedSummarizedExperiment-method}
\alias{distance,RangedSummarizedExperiment,RangedSummarizedExperiment-method}
\alias{distanceToNearest}
\alias{distanceToNearest,RangedSummarizedExperiment,ANY-method}
\alias{distanceToNearest,ANY,RangedSummarizedExperiment-method}
\alias{distanceToNearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method}
\title{Finding the nearest range neighbor in RangedSummarizedExperiment objects}
\description{
This man page documents the \code{nearest} methods and family (i.e.
\code{precede}, \code{follow}, \code{distance}, and \code{distanceToNearest}
methods) for \link{RangedSummarizedExperiment} objects.
}
\usage{
\S4method{precede}{RangedSummarizedExperiment,ANY}(x, subject, select=c("arbitrary", "all"),
ignore.strand=FALSE)
\S4method{precede}{ANY,RangedSummarizedExperiment}(x, subject, select=c("arbitrary", "all"),
ignore.strand=FALSE)
\S4method{follow}{RangedSummarizedExperiment,ANY}(x, subject, select=c("arbitrary", "all"),
ignore.strand=FALSE)
\S4method{follow}{ANY,RangedSummarizedExperiment}(x, subject, select=c("arbitrary", "all"),
ignore.strand=FALSE)
\S4method{nearest}{RangedSummarizedExperiment,ANY}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
\S4method{nearest}{ANY,RangedSummarizedExperiment}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
\S4method{distance}{RangedSummarizedExperiment,ANY}(x, y, ignore.strand=FALSE, ...)
\S4method{distance}{ANY,RangedSummarizedExperiment}(x, y, ignore.strand=FALSE, ...)
\S4method{distanceToNearest}{RangedSummarizedExperiment,ANY}(x, subject, ignore.strand=FALSE, ...)
\S4method{distanceToNearest}{ANY,RangedSummarizedExperiment}(x, subject, ignore.strand=FALSE, ...)
}
\arguments{
\item{x, subject}{
One of these two arguments must be a \link{RangedSummarizedExperiment}
object.
}
\item{select, ignore.strand}{
See \code{?\link[GenomicRanges]{nearest}} in the \pkg{GenomicRanges}
package.
}
\item{y}{
For the \code{distance} methods, one of \code{x} or \code{y} must be a
\link{RangedSummarizedExperiment} object.
}
\item{...}{Additional arguments for methods.}
}
\details{
These methods operate on the \code{rowRanges} component of the
\link{RangedSummarizedExperiment} object, which can be a
\link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
object.
More precisely, if any of the above functions is passed a
\link{RangedSummarizedExperiment} object thru the \code{x}, \code{subject},
and/or \code{y} argument, then it behaves as if \code{rowRanges(x)},
\code{rowRanges(subject)}, and/or \code{rowRanges(y)} had been passed
instead.
See \code{?\link[GenomicRanges]{nearest}} in the \pkg{GenomicRanges}
package for the details of how \code{nearest} and family operate on
\link[GenomicRanges]{GenomicRanges} and \link[GenomicRanges]{GRangesList}
objects.
}
\value{
See \code{?\link[GenomicRanges]{nearest}} in the \pkg{GenomicRanges}
package.
}
\seealso{
\itemize{
\item \link{RangedSummarizedExperiment} objects.
\item The \link[GenomicRanges]{nearest} man page in the
\pkg{GenomicRanges} package where the \code{nearest} family
of methods for \link[GenomicRanges]{GenomicRanges} and
\link[GenomicRanges]{GRangesList} objects is documented.
}
}
\examples{
nrows <- 20; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
IRanges(sample(1000L, 20), width=100),
strand=Rle(c("+", "-"), c(12, 8)))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowRanges=rowRanges, colData=colData)
rse1 <- shift(rse0, 100)
res <- nearest(rse0, rse1)
res
stopifnot(identical(res, nearest(rowRanges(rse0), rowRanges(rse1))))
stopifnot(identical(res, nearest(rse0, rowRanges(rse1))))
stopifnot(identical(res, nearest(rowRanges(rse0), rse1)))
res <- nearest(rse0) # missing subject
res
stopifnot(identical(res, nearest(rowRanges(rse0))))
hits <- nearest(rse0, rse1, select="all")
hits
stopifnot(identical(
hits,
nearest(rowRanges(rse0), rowRanges(rse1), select="all")
))
stopifnot(identical(
hits,
nearest(rse0, rowRanges(rse1), select="all")
))
stopifnot(identical(
hits,
nearest(rowRanges(rse0), rse1, select="all")
))
}
\keyword{methods}
\keyword{utilities}
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